cistematic/programs/cisGreedy.py

   1 ###########################################################################
   2 #                                                                         #
   3 # C O P Y R I G H T   N O T I C E                                         #
   4 #  Copyright (c) 2003-10 by:                                              #
   5 #    * California Institute of Technology                                 #
   6 #                                                                         #
   7 #    All Rights Reserved.                                                 #
   8 #                                                                         #
   9 # Permission is hereby granted, free of charge, to any person             #
  10 # obtaining a copy of this software and associated documentation files    #
  11 # (the "Software"), to deal in the Software without restriction,          #
  12 # including without limitation the rights to use, copy, modify, merge,    #
  13 # publish, distribute, sublicense, and/or sell copies of the Software,    #
  14 # and to permit persons to whom the Software is furnished to do so,       #
  15 # subject to the following conditions:                                    #
  16 #                                                                         #
  17 # The above copyright notice and this permission notice shall be          #
  18 # included in all copies or substantial portions of the Software.         #
  19 #                                                                         #
  20 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
  21 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
  22 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
  23 # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
  24 # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
  25 # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
  26 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
  27 # SOFTWARE.                                                               #
  28 ###########################################################################
  29 #
  30 # covariance.py
  31 from cistematic.programs import Program
  32 import time, Consensus
  33 from cistematic.core.motif import Motif
  34
  35
  36 class CisGreedy(Program):
  37
  38
  39     def getSettings(self):
  40         return (self.model, self.nmotifs, self.minwidth, self.maxwidth, self.bON,
  41                 self.iterations, self.Founder, self.bfile, self.percID,
  42                 self.founderPercID, self.MarkovSize)
  43
  44
  45     def setSettings(self, settings):
  46         self.motifs = []
  47         (self.model, self.nmotifs, self.minwidth, self.maxwidth, self.bON,
  48          self.iterations, self.Founder, self.bfile, self.percID,
  49         self.founderPercID, self.MarkovSize) = settings
  50
  51
  52     def setGenExpOptions(self, optionArray):
  53         self.setModel("zoops")
  54         self.setNumMotifs("10")
  55         self.setMaxWidth("15")
  56         self.setMinWidth("6")
  57         self.setBON(True)
  58         self.setIterations("100")
  59         self.bfile = "None"
  60         self.TCM="All"
  61         self.Founder = False
  62         self.setPercID("75")
  63         self.setMarkovSize("3")
  64         self.setFounderPID("75")
  65         self.setBackground("None")
  66         for option in optionArray:
  67             (optionTag, optionValue) = option.split(":")
  68
  69             if optionTag == "Markov size":
  70                 self.setMarkovSize(optionValue)
  71
  72             if optionTag == "percentID":
  73                 self.setPercID(optionValue)
  74
  75             if optionTag == "founderPercentID":
  76                 self.setFounderPID(optionValue)
  77
  78             if optionTag == "model":
  79                 self.setModel(optionValue)
  80
  81             if optionTag == "nmotifs":
  82                 self.setNumMotifs(optionValue)
  83
  84             if optionTag == "width":
  85                 self.setMinWidth(optionValue)
  86                 self.setMaxWidth(optionValue)
  87
  88             if optionTag == "minWidth":
  89                 self.setMinWidth(optionValue)
  90
  91             if optionTag == "maxWidth":
  92                 self.setMaxWidth(optionValue)
  93
  94             if optionTag == "reverse":
  95                 self.setBON(optionValue)
  96
  97             if optionTag == "iterations":
  98                 self.setIterations(optionValue)
  99
 100             if optionTag == "background":
 101                 self.setBackground(optionValue)
 102
 103             if optionTag == "founder":
 104                 self.setFounder(True)
 105
 106         #if no background file is provided the default setting
 107         #is to use the input sequences as a background
 108         print self.bfile
 109         #set markovSize
 110
 111
 112     def setMarkovSize(self, val):
 113         self.MarkovSize = int(str(val))
 114
 115
 116     def setFounderPID(self, val):
 117         self.founderPercID = int(str(val))
 118
 119
 120     def setFounder(self, boolVal):
 121         if boolVal:
 122             self.Founder = True
 123         else:
 124             self.Founder = False
 125
 126
 127     def setPercID(self, percVal):
 128         self.percID = int(str(percVal))
 129
 130
 131     def setModel(self, modelType):
 132         if modelType in ["oops", "zoops", "tcm"]:
 133             self.model = str(modelType)
 134         else:
 135             self.model = "zoops";
 136
 137
 138     def setIterations(self, number):
 139         self.iterations = int(str(number))
 140
 141
 142     def setNumMotifs(self, motifNum):
 143         self.nmotifs = int(str(motifNum))
 144
 145
 146     def setBON(self, B_val):
 147         if str(B_val) == "False":
 148             self.bON = False
 149         else:
 150             self.bON = True
 151
 152
 153     def getSequences(self, infile):
 154         seqFiles = open(infile, 'r')
 155         Lines = seqFiles.readlines()
 156         seqFiles.close()
 157         self.sequences = []
 158         for line in Lines:
 159             if line[0] != ">":
 160                 self.sequences.append(line[:-1])
 161
 162
 163     def setMinWidth(self, width):
 164         self.minwidth = int(str(width))
 165
 166
 167     def setMaxWidth(self, width):
 168         self.maxwidth = int(str(width))
 169
 170
 171     def setBackground(self, backFile):
 172         self.bfile = str(backFile)
 173
 174
 175     def run(self):
 176         print self.nmotifs
 177         startTime = time.time()
 178         if self.bfile == "None":
 179             self.bfile = Consensus.Markov(self.sequences, self.bON,self.MarkovSize)
 180
 181         print "geting consensus score"
 182         self.contents = Consensus.MotifFinder(self.sequences, self.minwidth, self.maxwidth,
 183                                               self.nmotifs, self.iterations, self.bfile,
 184                                               self.bON, self.Founder,self.percID,
 185                                               self.founderPercID, self.MarkovSize, self.model,
 186                                               self.TCM)
 187         stopTime = time.time()
 188         print "\nThis run took %.3f - %.3f = %.3f seconds and produced %d motifs" % (startTime, stopTime, stopTime - startTime, len(self.contents[0]))
 189
 190
 191     def getMotifs(self):
 192         self.motifs = []
 193         try:
 194             (PWMs, Seqs) = self.contents
 195             for index in range(len(Seqs)):
 196                 self.motifs.append(Motif("%s-cisGreedy-%s" % (self.tagID, str(index + 1)), seqs=Seqs[index]))
 197         except:
 198             print "error returning motifs"
 199             pass
 200
 201         return self.motifs